FXR1 FMR1 autosomal homolog 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: FXR1provided by HGNC
Official Full Name: FMR1 autosomal homolog 1provided by HGNC
Primary source: HGNC:HGNC:4023
See related: Ensembl:ENSG00000114416 MIM:600819; AllianceGenome:HGNC:4023
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: FXR1P; CMYP9A; CMYP9B; MYOPMIL; MYORIBF
Summary: The protein encoded by this gene is an RNA binding protein that interacts with the functionally-similar proteins FMR1 and FXR2. These proteins shuttle between the nucleus and cytoplasm and associate with polyribosomes, predominantly with the 60S ribosomal subunit. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 27.2), ovary (RPKM 11.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q26.33

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (180912670..180982753)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (183714436..183784535)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (180630458..180700541)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

LLPS of FXR proteins drives replication organelle clustering for beta-coronaviral proliferation.
Title: LLPS of FXR proteins drives replication organelle clustering for β-coronaviral proliferation.
The multifaceted role of Fragile X-Related Protein 1 (FXR1) in cellular processes: an updated review on cancer and clinical applications.
Title: The multifaceted role of Fragile X-Related Protein 1 (FXR1) in cellular processes: an updated review on cancer and clinical applications.
FXR1 regulates vascular smooth muscle cell cytoskeleton, VSMC contractility, and blood pressure by multiple mechanisms.
Title: FXR1 regulates vascular smooth muscle cell cytoskeleton, VSMC contractility, and blood pressure by multiple mechanisms.
Fragile X-Related Protein FXR1 Controls Human Adenovirus Capsid mRNA Metabolism.
Title: Fragile X-Related Protein FXR1 Controls Human Adenovirus Capsid mRNA Metabolism.
FXR1 facilitates axitinib resistance in clear cell renal cell carcinoma via regulating KEAP1/Nrf2 signaling pathway.
Title: FXR1 facilitates axitinib resistance in clear cell renal cell carcinoma via regulating KEAP1/Nrf2 signaling pathway.
FMRP, FXR1 protein and Dlg4 mRNA, which are associated with fragile X syndrome, are involved in the ubiquitin-proteasome system.
Title: FMRP, FXR1 protein and Dlg4 mRNA, which are associated with fragile X syndrome, are involved in the ubiquitin-proteasome system.
Exosomal circZNF451 restrains anti-PD1 treatment in lung adenocarcinoma via polarizing macrophages by complexing with TRIM56 and FXR1.
Title: Exosomal circZNF451 restrains anti-PD1 treatment in lung adenocarcinoma via polarizing macrophages by complexing with TRIM56 and FXR1.
CircSETD3 mediates acquired resistance to gefitinib in non-small lung cancer cells by FXR1/ECT2 pathway.
Title: CircSETD3 mediates acquired resistance to gefitinib in non-small lung cancer cells by FXR1/ECT2 pathway.
FXR1-related congenital myopathy: expansion of the clinical and genetic spectrum.
Title: FXR1-related congenital myopathy: expansion of the clinical and genetic spectrum.
CEP63 upregulates YAP1 to promote colorectal cancer progression through stabilizing RNA binding protein FXR1.
Title: CEP63 upregulates YAP1 to promote colorectal cancer progression through stabilizing RNA binding protein FXR1.

Submit: New GeneRIF Correction See all GeneRIFs (58)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Myopathy, congenital proximal, with minicore lesions MedGen: C5394193 OMIM: 618823 GeneReviews: Not available	Compare labs
Myopathy, congenital, with respiratory insufficiency and bone fractures MedGen: C5394189 OMIM: 618822 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of fragile X mental retardation, autosomal homolog 1 (FXR1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	Interaction of HIV-1 Gag with fragile X mental retardation, autosomal homolog 1 (FXR1) is identified in a series of six affinity purification/mass spectrometry screens	PubMed
Tat	tat	Fragile X mental retardation, autosomal homolog 1 (FXR1) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS/MS	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G60386 (e-PCR)
- UniSTS:137492

BI274570 (e-PCR)
- UniSTS:249125

SHGC-77579 (e-PCR)
- UniSTS:32551

SHGC-77583 (e-PCR)
- UniSTS:59962

BI281166 (e-PCR)
- UniSTS:249408

RH98363 (e-PCR)
- UniSTS:89700

Cda01e11 (e-PCR)
- UniSTS:64869

D3S2910E (e-PCR)
- UniSTS:150894

Fxr1h (e-PCR), detects polymorphism
- UniSTS:498301

D3S3105 (e-PCR)
- UniSTS:61824

SHGC-53644 (e-PCR)
- UniSTS:76162

FXR1 (e-PCR)
- UniSTS:505522

A006P45 (e-PCR)
- UniSTS:58844

RH123299 (e-PCR)
- UniSTS:135676

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables RNA strand annealing activity	IDA Inferred from Direct Assay more info	PubMed
enables mRNA 3'-UTR AU-rich region binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA 3'-UTR binding	IBA Inferred from Biological aspect of Ancestor more info
enables mRNA 3'-UTR binding	IDA Inferred from Direct Assay more info	PubMed
enables molecular condensate scaffold activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables ribosome binding	IEA Inferred from Electronic Annotation more info
enables translation regulator activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in animal organ development	IBA Inferred from Biological aspect of Ancestor more info
involved_in apoptotic process	TAS Traceable Author Statement more info	PubMed
involved_in dentate gyrus development	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA destabilization	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in muscle organ development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of inflammatory response	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of long-term synaptic potentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of translation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of tumor necrosis factor production	ISS Inferred from Sequence or Structural Similarity more info
involved_in non-membrane-bounded organelle assembly	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in nuclear pore complex assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in nuclear pore localization	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of long-term neuronal synaptic plasticity	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of miRNA-mediated gene silencing	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of translation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of translation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of circadian sleep/wake cycle, sleep	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of mRNA stability	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of neurogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of synaptic transmission, glutamatergic	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of translation at presynapse, modulating synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal muscle organ development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spermatid development	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Component	Evidence Code	Pubs
located_in costamere	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in cytoplasmic ribonucleoprotein granule	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasmic stress granule	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasmic stress granule	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in intracellular non-membrane-bounded organelle	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in membrane	HDA more info	PubMed
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nuclear envelope	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	TAS Traceable Author Statement more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in ribosome	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: RNA-binding protein FXR1

Names: FMR1 autosomal protein-like protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001013438.3 → NP_001013456.1 RNA-binding protein FXR1 isoform b

See identical proteins and their annotated locations for NP_001013456.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate exon compared to variant 1, that causes a frameshift. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.

Source sequence(s)

AC008009, AK225334, DC352767

Consensus CDS

CCDS46965.1

UniProtKB/TrEMBL

B4DM21

Related

ENSP00000388828.2, ENST00000445140.6

Conserved Domains (7) summary

pfam12235
Location:354 → 436

FXMRP1_C_core; Fragile X-related 1 protein core C terminal

pfam16096
Location:462 → 535

FXR_C1; Fragile X-related 1 protein C-terminal region 2

cd20472
Location:3 → 57

Tudor_Agenet_FXR1_rpt1; first Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd20475
Location:61 → 126

Tudor_Agenet_FXR1_rpt2; second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22504
Location:123 → 199

KH_I_FXR1_rpt1; first type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22507
Location:218 → 280

KH_I_FXR1_rpt2; second type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22510
Location:281 → 358

KH_I_FXR1_rpt3; third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins
NM_001013439.3 → NP_001013457.1 RNA-binding protein FXR1 isoform c

See identical proteins and their annotated locations for NP_001013457.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a.

Source sequence(s)

AC008009, AK292633, AU280585, DC352767

Consensus CDS

CCDS33894.1

UniProtKB/TrEMBL

B4DM78

Related

ENSP00000307633.7, ENST00000305586.11

Conserved Domains (7) summary

pfam12235
Location:269 → 351

FXMRP1_C_core; Fragile X-related 1 protein core C terminal

pfam16096
Location:377 → 450

FXR_C1; Fragile X-related 1 protein C-terminal region 2

pfam16097
Location:469 → 535

FXR_C3; Fragile X-related 1 protein C-terminal region 3

cd22504
Location:38 → 114

KH_I_FXR1_rpt1; first type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22507
Location:133 → 195

KH_I_FXR1_rpt2; second type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22510
Location:196 → 273

KH_I_FXR1_rpt3; third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cl02573
Location:1 → 41

Tudor_SF; Tudor domain superfamily
NM_001363882.1 → NP_001350811.1 RNA-binding protein FXR1 isoform d

Status: REVIEWED

Source sequence(s)

AC008009

Consensus CDS

CCDS87169.1

UniProtKB/TrEMBL

B4DGH9, E7EU85

Related

ENSP00000420515.1, ENST00000468861.5

Conserved Domains (6) summary

pfam12235
Location:269 → 351

FXMRP1_C_core; Fragile X-related 1 protein core C terminal

pfam16096
Location:377 → 450

FXR_C1; Fragile X-related 1 protein C-terminal region 2

cd22504
Location:38 → 114

KH_I_FXR1_rpt1; first type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22507
Location:133 → 195

KH_I_FXR1_rpt2; second type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22510
Location:196 → 273

KH_I_FXR1_rpt3; third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cl02573
Location:1 → 41

Tudor_SF; Tudor domain superfamily
NM_005087.4 → NP_005078.2 RNA-binding protein FXR1 isoform a

See identical proteins and their annotated locations for NP_005078.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (a).

Source sequence(s)

AC008009, AK292633, DC352767

Consensus CDS

CCDS3238.1

UniProtKB/Swiss-Prot

A8K9B8, P51114, Q7Z450, Q8N6R8

UniProtKB/TrEMBL

B4DXZ6

Related

ENSP00000350170.3, ENST00000357559.9

Conserved Domains (8) summary

pfam12235
Location:354 → 436

FXMRP1_C_core; Fragile X-related 1 protein core C terminal

pfam16096
Location:462 → 535

FXR_C1; Fragile X-related 1 protein C-terminal region 2

pfam16097
Location:554 → 620

FXR_C3; Fragile X-related 1 protein C-terminal region 3

cd20472
Location:3 → 57

Tudor_Agenet_FXR1_rpt1; first Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd20475
Location:61 → 126

Tudor_Agenet_FXR1_rpt2; second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22504
Location:123 → 199

KH_I_FXR1_rpt1; first type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22507
Location:218 → 280

KH_I_FXR1_rpt2; second type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins

cd22510
Location:281 → 358

KH_I_FXR1_rpt3; third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins